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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ), 'gf_id' => 'HOM05D001494', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001494' ), 'data_identifier' => 'HOM05D001494', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001494', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '424', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38330' => 'bna', 'A06p37990' => 'bna', 'A09p04940' => 'bna', 'A09p68940' => 'bna', 'A10p00750' => 'bna', 'Aa31LG11G8670' => 'aar', 'Aa31LG1G10530' => 'aar', 'Aa31LG5G1080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3347' => 'aag', 'Actinidia03298' => 'ach', 'Actinidia07997' => 'ach', 'Actinidia08688' => 'ach', 'Actinidia20278' => 'ach', 'Ah.05g179100' => 'amhyb', 'Ah.06g192020' => 'amhyb', 'AL1G11340' => 'aly', 'AL6G40650' => 'aly', 'AL6G52610' => 'aly', 'Aqoxy5G00296' => 'aox', 'Aqoxy5G04338' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0T87WI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2XE8WN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71F8WW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8236ZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HK1F5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L225S3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3QUTI' => 'arhy', 'AT1G01160' => 'ath', 'AT4G00850' => 'ath', 'AT5G28640' => 'ath', 'ATR0090G014' => 'atr', 'ATR1125G089' => 'atr', 'Atru.chr2.881' => 'acertr', 'Atru.chr5.747' => 'acertr', 'AUR62004547' => 'cqu', 'AUR62004889' => 'cqu', 'AUR62006021' => 'cqu', 'AUR62022661' => 'cqu', 'AUR62035605' => 'cqu', 'BcaB03g13561' => 'bca', 'BcaB04g19624' => 'bca', 'BcaB04g19626' => 'bca', 'BcaB07g33887' => 'bca', 'BcaB07g34177' => 'bca', 'BcaC03g17754' => 'bca', 'BcaC04g23724' => 'bca', 'BcaNung01726' => 'bca', 'BcaNung02101' => 'bca', 'BolC2t11839H' => 'bol', 'BolC5t28862H' => 'bol', 'BolC7t44559H' => 'bol', 'BolC8t52868H' => 'bol', 'BolC9t53461H' => 'bol', 'BraA02t08814Z' => 'bra', 'BraA06t26715Z' => 'bra', 'BraA09t36133Z' => 'bra', 'BraA09t42234Z' => 'bra', 'BraA10t42351Z' => 'bra', 'C02p57670' => 'bna', 'C05p00780' => 'bna', 'C07p40240' => 'bna', 'C08p53530' => 'bna', 'C09p05340' => 'bna', 'CAN.G1256.2' => 'can', 'CAN.G1347.6' => 'can', 'CAN.G186.69' => 'can', 'CAN.G271.5' => 'can', 'CAN.G358.148' => 'can', 'CANSAT11G1826' => 'cansat', 'CANSAT21G1574' => 'cansat', 'CANSAT54G2344' => 'cansat', 'CARHR001310' => 'chi', 'CARHR185230' => 'chi', 'CARHR249480' => 'chi', 'Carub.0001s0105' => 'cru', 'Carub.0006s2591' => 'cru', 'Carub.0006s3587' => 'cru', 'Ca_09434_v3' => 'car', 'Ca_10032_v3' => 'car', 'Ca_16757_v3' => 'car', 'Ca_23493_v3' => 'car', 'Ca_29945_v3' => 'car', 'Cc02_g00950' => 'ccan', 'Cc02_g09130' => 'ccan', 'Cc02_g39850' => 'ccan', 'CDE03G0198' => 'cde', 'CDE03G0506' => 'cde', 'CDE04G0014' => 'cde', 'CDE04G2549' => 'cde', 'CDE06G0532' => 'cde', 'CDE07G0517' => 'cde', 'Cfa006389' => 'cfa', 'Ciclev10022144m.g' => 'ccl', 'Ciclev10022233m.g' => 'ccl', 'CiPaw.01G080800' => 'cil', 'CiPaw.02G044200' => 'cil', 'CiPaw.05G203000' => 'cil', 'CiPaw.07G070300' => 'cil', 'CiPaw.08G119400' => 'cil', 'ClCG02G016890' => 'cla', 'ClCG11G006560' => 'cla', 'COL.COLO4_06219' => 'col', 'COL.COLO4_14352' => 'col', 'COL.COLO4_15408' => 'col', 'COL.COLO4_15409' => 'col', 'Cpa.g.c27606.1' => 'cpa', 'Cpa.g.sc141.17' => 'cpa', 'Cpa.g.sc162.7' => 'cpa', 'Cre01.g055200' => 'cre', 'CsaV3_2G003880' => 'csa', 'CsaV3_6G001440' => 'csa', 'CSS0012368' => 'camsi', 'CSS0015323' => 'camsi', 'CSS0035099' => 'camsi', 'CSS0037209' => 'camsi', 'CSS0050322' => 'camsi', 'DCAR_006989' => 'dca', 'DCAR_008968' => 'dca', 'DCAR_008969' => 'dca', 'DCAR_012526' => 'dca', 'DCAR_014558' => 'dca', 'DCAR_014559' => 'dca', 'DCAR_028383' => 'dca', 'Dinv05727' => 'din', 'Dinv22450' => 'din', 'Dinv29225' => 'din', 'Dinv30122' => 'din', 'Dinv32635' => 'din', 'Dinv34249' => 'din', 'Duzib068G0628' => 'dzi', 'Duzib084G0170' => 'dzi', 'Duzib106G1326' => 'dzi', 'Duzib133G0286' => 'dzi', 'Duzib138G1081' => 'dzi', 'Duzib177G0505' => 'dzi', 'Duzib205G1565' => 'dzi', 'Duzib268G0406' => 'dzi', 'ECA232G3238' => 'eca', 'ECA233G0782' => 'eca', 'ECA236G3483' => 'eca', 'ECA238G3537' => 'eca', 'ECA247G1683' => 'eca', 'EL10Ac1g00201' => 'bvu', 'EL10Ac3g05200' => 'bvu', 'EL10Ac4g09046' => 'bvu', 'Eucgr.B02127' => 'egr', 'Eucgr.H04262' => 'egr', 'Eucgr.L00737' => 'egr', 'FAN01G2795' => 'fan', 'FAN02G4133' => 'fan', 'FAN03G1664' => 'fan', 'FAN05G1638' => 'fan', 'FAN05G3907' => 'fan', 'FAN06G0420' => 'fan', 'FAN06G3080' => 'fan', 'FAN09G0085' => 'fan', 'FAN10G0868' => 'fan', 'FAN10G2837' => 'fan', 'FAN14G1685' => 'fan', 'FAN14G4019' => 'fan', 'FvH4_6g02460' => 'fve', 'FvH4_7g17400' => 'fve', 'Glyma.03G249000' => 'gma', 'Glyma.06G134400' => 'gma', 'Glyma.07G051300' => 'gma', 'Glyma.08G221100' => 'gma', 'Glyma.10G164100' => 'gma', 'Glyma.16G020400' => 'gma', 'Glyma.19G246600' => 'gma', 'Glyma.20G226500' => 'gma', 'Gohir.A03G051100' => 'ghi', 'Gohir.A08G216900' => 'ghi', 'Gohir.A11G250400' => 'ghi', 'Gohir.A11G250520' => 'ghi', 'Gohir.A12G115500' => 'ghi', 'Gohir.A12G115700' => 'ghi', 'Gohir.A13G169000' => 'ghi', 'Gohir.D03G116600' => 'ghi', 'Gohir.D08G233900' => 'ghi', 'Gohir.D11G261100' => 'ghi', 'Gohir.D12G119100' => 'ghi', 'Gohir.D12G119300' => 'ghi', 'Gohir.D13G174400' => 'ghi', 'Gorai.003G122900' => 'gra', 'Gorai.004G248600' => 'gra', 'Gorai.007G279600' => 'gra', 'Gorai.008G129100' => 'gra', 'Gorai.008G129300' => 'gra', 'Gorai.013G186300' => 'gra', 'GSVIVG01027418001' => 'vvi', 'GSVIVG01028287001' => 'vvi', 'GSVIVG01036262001' => 'vvi', 'GSVIVG01038626001' => 'vvi', 'HanXRQChr05g0139311' => 'han', 'HanXRQChr07g0200601' => 'han', 'HanXRQChr08g0217191' => 'han', 'HanXRQChr08g0225711' => 'han', 'HanXRQChr10g0281161' => 'han', 'HanXRQChr14g0455321' => 'han', 'HanXRQChr15g0480541' => 'han', 'Haze_04387' => 'cav', 'Haze_15714' => 'cav', 'Hma1.2p1_0180F.1_g079880' => 'hma', 'Hma1.2p1_0345F.1_g131270' => 'hma', 'Hma1.2p1_0415F.1_g148100' => 'hma', 'HPP92_009423' => 'vpl', 'HPP92_010441' => 'vpl', 'Hund09701' => 'sun', 'Hund16741' => 'sun', 'Hund27158' => 'sun', 'Hund28885' => 'sun', 'Hund28886' => 'sun', 'Lalb_Chr04g0254231' => 'lal', 'Lalb_Chr06g0168171' => 'lal', 'Lalb_Chr06g0171791' => 'lal', 'Lalb_Chr06g0171801' => 'lal', 'Lalb_Chr10g0100811' => 'lal', 'Lalb_Chr11g0067281' => 'lal', 'Lalb_Chr17g0342941' => 'lal', 'Lalb_Chr18g0044001' => 'lal', 'Lalb_Chr18g0044011' => 'lal', 'Lalb_Chr21g0311081' => 'lal', 'Lj1A62G11' => 'lonja', 'Lj1g0006751' => 'lja', 'Lj1g0018088' => 'lja', 'Lj2C38G3' => 'lonja', 'Lj3C917T8' => 'lonja', 'Lj3g0005361' => 'lja', 'Lj5g0004761' => 'lja', 'Lj9A604T65' => 'lonja', 'Lsat_1_v5_gn_2_107500' => 'lsa', 'Lsat_1_v5_gn_2_28520' => 'lsa', 'Lsat_1_v5_gn_3_74940' => 'lsa', 'Lsat_1_v5_gn_5_105161' => 'lsa', 'Lsat_1_v5_gn_6_17540' => 'lsa', 'Lsat_1_v5_gn_7_36161' => 'lsa', 'Lsat_1_v5_gn_8_24961' => 'lsa', 'Lsat_1_v5_gn_9_50160' => 'lsa', 'Lsat_1_v5_gn_9_9381' => 'lsa', 'Manes.01G041400' => 'mes', 'Manes.01G241400' => 'mes', 'Manes.05G018100' => 'mes', 'Manes.08G136900' => 'mes', 'Manes.09G150200' => 'mes', 'Mapoly0047s0121' => 'mpo', 'MBI04_g00952_MAGBIO' => 'mbi', 'MBI04_g10916_MAGBIO' => 'mbi', 'MBI06_g06410_MAGBIO' => 'mbi', 'MBI07_g39809_MAGBIO' => 'mbi', 'MBI11_g40181_MAGBIO' => 'mbi', 'MBI18_g32817_MAGBIO' => 'mbi', 'MCO11G859' => 'mco', 'MD01G1087000' => 'mdo', 'MD04G1227900' => 'mdo', 'MD07G1157100' => 'mdo', 'MD07G1157200' => 'mdo', 'MD12G1244500' => 'mdo', 'Medtr1g080590' => 'mtr', 'Medtr3g092260' => 'mtr', 'Medtr3g097190' => 'mtr', 'Medtr7g115410' => 'mtr', 'Medtr8g024650' => 'mtr', 'Medtr8g072930' => 'mtr', 'MELO3C004407.2' => 'cme', 'MELO3C008248.2' => 'cme', 'Migut.F00821' => 'egut', 'Migut.F00996' => 'egut', 'Migut.N01521' => 'egut', 'MSTRG.26988' => 'ama', 'MSTRG.4796' => 'ama', 'MSTRG.8541' => 'ama', 'MSTRG.9010' => 'ama', 'Nitab4.5_0000319g0250' => 'nta', 'Nitab4.5_0000768g0010' => 'nta', 'Nitab4.5_0000930g0090' => 'nta', 'Nitab4.5_0001117g0090' => 'nta', 'Nitab4.5_0001993g0030' => 'nta', 'Nitab4.5_0002640g0040' => 'nta', 'Nitab4.5_0003799g0020' => 'nta', 'Nitab4.5_0007901g0050' => 'nta', 'Nn1g02660' => 'nnu', 'Nn3g18835' => 'nnu', 'Nn3g19574' => 'nnu', 'Oeu007905.1' => 'oeu', 'Oeu016031.1' => 'oeu', 'Oeu022738.1' => 'oeu', 'Oeu031436.1' => 'oeu', 'Oeu033257.1' => 'oeu', 'Oeu037967.1' => 'oeu', 'Oeu042965.1' => 'oeu', 'Oeu055179.1' => 'oeu', 'Os03g0733600' => 'osa', 'Os11g0615200' => 'osa', 'Os12g0496900' => 'osa', 'Peaxi162Scf00087g00083' => 'pax', 'Peaxi162Scf00120g00067' => 'pax', 'Peaxi162Scf00135g01012' => 'pax', 'Peaxi162Scf00542g00625' => 'pax', 'Peaxi162Scf00740g00550' => 'pax', 'Peaxi162Scf00767g00418' => 'pax', 'PGR102G3010' => 'pgr', 'PGR142G1355' => 'pgr', 'PGSC0003DMG400000988' => 'stu', 'PGSC0003DMG400003212' => 'stu', 'PGSC0003DMG400005527' => 'stu', 'PGSC0003DMG401025427' => 'stu', 'Phvul.006G103700' => 'pvu', 'Phvul.007G189200' => 'pvu', 'Phvul.008G253900' => 'pvu', 'Phvul.009G050300' => 'pvu', 'Phvul.010G118100' => 'pvu', 'Potri.002G177600' => 'ptr', 'Potri.012G023100' => 'ptr', 'Potri.013G043700' => 'ptr', 'Potri.014G103900' => 'ptr', 'Potri.019G013100' => 'ptr', 'Pp3c13_15090' => 'ppa', 'Pp3c13_2290' => 'ppa', 'Pp3c3_21060' => 'ppa', 'Pp3c3_5580' => 'ppa', 'Prupe.2G195600' => 'ppe', 'Prupe.6G346900' => 'ppe', 'Psat0s1452g0040' => 'psa', 'Psat0s2429g0080' => 'psa', 'Psat0s3277g0080' => 'psa', 'Psat0s368g0160' => 'psa', 'Psat2g088680' => 'psa', 'Psat4g217040' => 'psa', 'PSO210G4488' => 'pso', 'PSO349G0314' => 'pso', 'PSO765G0010' => 'pso', 'PSO801G0057' => 'pso', 'PSO832G0149' => 'pso', 'QL03p028987' => 'qlo', 'QL08p046724' => 'qlo', 'QL09p007387' => 'qlo', 'QL93p0214_0033' => 'qlo', 'RcHm_v2.0_Chr1g0360841' => 'rch', 'RcHm_v2.0_Chr3g0450341' => 'rch', 'Rhsim05G0176000' => 'rsi', 'Sabra12G0010800' => 'sbr', 'Sabra13G0040500' => 'sbr', 'Sabra14G0076400' => 'sbr', 'Sabra15G0004600' => 'sbr', 'Sabra19G0017000' => 'sbr', 'Sabra19G0026200' => 'sbr', 'SalBow2G0299' => 'sbo', 'SalBow5G3641' => 'sbo', 'Sc09g0004090' => 'sci', 'Sc13g0010160' => 'sci', 'Sc20g0000490' => 'sci', 'Sc26g0000470' => 'sci', 'Sed0008028' => 'sed', 'Sed0019691' => 'sed', 'Sed0021193' => 'sed', 'SEGI_14183' => 'sgi', 'SEGI_25274' => 'sgi', 'SEGI_29100' => 'sgi', 'SEGI_30560' => 'sgi', 'SGA_v2.0_scaffold141G35541' => 'sas', 'SGA_v2.0_scaffold43G16344' => 'sas', 'SHI18467' => 'shi', 'SMO142G0065' => 'smo', 'SMO172G0229' => 'smo', 'SMO198G0012' => 'smo', 'SMO358G0689' => 'smo', 'Solyc03g082480.4' => 'sly', 'Solyc04g009820.3' => 'sly', 'Solyc10g009280.4' => 'sly', 'Solyc11g006230.3' => 'sly', 'Sopen03g022210' => 'spe', 'Sopen04g004950' => 'spe', 'Sopen10g005060' => 'spe', 'Sopen11g002150' => 'spe', 'Sp1g01130' => 'spa', 'Sp2g20130' => 'spa', 'Sp6g01270' => 'spa', 'TAR365G1012' => 'tar', 'TAR374G0533' => 'tar', 'TAR406G0006' => 'tar', 'TAR633G0935' => 'tar', 'TAR633G1765' => 'tar', 'TAR636G3277' => 'tar', 'THA.LOC104799252' => 'tha', 'THA.LOC104801351' => 'tha', 'THA.LOC104802838' => 'tha', 'THA.LOC104815891' => 'tha', 'THA.LOC104825894' => 'tha', 'Thecc.01G335400' => 'tca', 'Thecc.03G206800' => 'tca', 'Thecc.05G277400' => 'tca', 'Thhalv10004925m.g' => 'esa', 'Thhalv10008482m.g' => 'esa', 'Thhalv10028952m.g' => 'esa', 'TPR.G14846' => 'tpr', 'TPR.G15142' => 'tpr', 'TPR.G25262' => 'tpr', 'TPR.G26642' => 'tpr', 'TPR.G39291' => 'tpr', 'TPR.G6917' => 'tpr', 'TWI12G0628' => 'twi', 'TWI14G1290' => 'twi', 'TWI31G0504' => 'twi', 'TWI32G1287' => 'twi', 'TWI56G0132' => 'twi', 'TWI56G1137' => 'twi', 'TWI59G0773' => 'twi', 'TWI63G0621' => 'twi', 'unitig_21.g20558' => 'ugi', 'unitig_32.g10675' => 'ugi', 'unitig_52.g16864' => 'ugi', 'unitig_744.g24022' => 'ugi', 'unitig_748.g8686' => 'ugi', 'vmacro12651' => 'vma', 'vmacro20007' => 'vma', 'VMungo0331G1691' => 'vmu', 'VMungo0540G0407' => 'vmu', 'VMungo0647G1256' => 'vmu', 'VMungo0720G1367' => 'vmu', 'VMungo1309G1372' => 'vmu', 'Zm00001eb056300' => 'zma', 'Zm00001eb138150' => 'zma', 'Zm00001eb166790' => 'zma', 'Zm00001eb409680' => 'zma' ) $gf_id = 'HOM05D001494' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001494' ) $data_identifier = 'HOM05D001494' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 2, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 6, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 1, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 8, 'ugi' => (int) 5, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409680' $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